Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics
Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics
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DOI：
10.1016/j.celrep.2015.01.008
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发表时间：
2015-02-10
期刊：
影响因子：
8.8
通讯作者：
Oliviero, Salvatore
中科院分区：
文献类型：
--
作者：
Neri, Francesco;Incarnato, Danny;Oliviero, Salvatore
10种11易位（泰特）蛋白将5-甲基胞嘧啶（5 mC）氧化为5-羟甲基胞嘧啶（5 hmC）、5-甲酰基胞嘧啶（5 fC）和5-羧基胞嘧啶（5caC）。5 fC和5caC可被胸腺嘧啶-DNA糖基化酶（Tdg）进一步切除。在这里，我们提出了一种全基因组的方法，称为甲基化辅助亚硫酸氢盐测序（MAB-seq），使5 fC和5caC的单碱基分辨率映射和测量它们的丰度。将该方法应用于小鼠胚胎干细胞（ESC）显示在高度表达基因的低甲基化启动子上存在5 fC和5caC残基，其在Tdg沉默后增加，揭示了这些启动子上的活性DNA去甲基化。Tdg的全基因组定位揭示了与Tet 1在活性启动子上的广泛共定位。发现这些区域被Dnmt 1和Dnmt 3a甲基化，并通过Tet-dependent机制去甲基化。我们的工作证明了DNA甲基化动力学，发生在表达基因的启动子上，并提供了一个基因组参考图谱的5 fC和5caC在胚胎干细胞。
Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-seq), that enables single-base resolution mapping of 5fC and 5caC and measures their abundance. Application of this method to mouse embryonic stem cells (ESCs) shows the occurrence of 5fC and 5caC residues on the hypomethylated promoters of highly expressed genes, which is increased upon Tdg silencing, revealing active DNA demethylation on these promoters. Genome-wide mapping of Tdg reveals extensive colocalization with Tet1 on active promoters. These regions were found to be methylated by Dnmt1 and Dnmt3a and demethylated by a Tet-dependent mechanism. Our work demonstrates the DNA methylation dynamics that occurs on the promoters of the expressed genes and provides a genomic reference map of 5fC and 5caC in ESCs.